I put together my build about a month ago and was not too happy with the temps (idle 50 C) i was getting on stock so I upgraded to a Zalman 9700 LED yesterday. I now idle at around 45-46 C and when running games, my cpu gets even hotter sometimes than it did with stock cooling. Why is this? I even applied arctic silver 5 instead of the zalman thermal compound.

Is any one else having these kinds of problems or does anything know what I should do?

it's more common for people to over apply AS5, they don't understand that it's actually a poor conductor of heat and is only there to keep air out which is even worse. follow the same instructions for applying AS5 to any processor with an IHS (Integrated Heat Spreader, the cap on top of the processor) for a quad core as it spreads over an area more than sufficient for the 4 cores.